diffreport-methods(xcms)
diffreport-methods()所属R语言包：xcms
Create report of analyte differences
创建报告分析物的差异
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Create a report showing the most significant differences between two sets of samples. Optionally create extracted ion chromatograms for the most significant differences.
创建一个报告显示，两组样品之间的最显着的差异。选择创建的最显着的差异提取离子色谱。
参数----------Arguments----------
参数：object
the xcmsSet object
xcmsSet对象
参数：class1
character vector with the first set of sample classes to be compared
与第一组样本类的字符向量进行比较
参数：class2
character vector with the second set of sample classes to be compared
字符与第二组样品类向量相比
参数：filebase
base file name to save report, .tsv file and _eic will be appended to this name for the tabular report and EIC directory, respectively. if blank nothing will be saved
基本文件名保存报告，.tsv文件和_eic将追加到这个名字的表格报告和EIC目录，分别。如果空白将被保存任何
参数：eicmax
number of the most significantly different analytes to create EICs for
最显着不同的分析物的数量，以创建EICs
参数：eicwidth
width (in seconds) of EICs produced
生产宽度的EICs（秒）
参数：sortpval
logical indicating whether the reports should be sorted by p-value
逻辑说明报告是否应当由p值排序
参数：classeic
character vector with the sample classes to include in the EICs
样本类的字符向量包括在EICs的
参数：value
intensity values to be used for the diffreport. <br> If value="into", integrated peak intensities are used. <br> If value="maxo", maximum peak intensities are used. <br> If value="intb", baseline corrected integrated peak intensities are used (only available if peak detection was done by findPeaks.centWave).
为diffreport强度值。如果value="into"，综合峰强度的参考。如果value="maxo"，最大峰值强度的参考。 <br>如果value="intb"，基线校正集成峰强度（仅当峰值检测findPeaks.centWave）。
参数：metlin
mass uncertainty to use for generating link to Metlin metabolite database. the sign of the uncertainty indicates negative or positive mode data for M+H or M-H calculation. a value of FALSE or 0 removes the column
质量的不确定性，使用生成链接METLIN代谢物数据库。不确定性的迹象表明消极或积极为M + H或MH计算模式的数据。 FALSE或0的值删除列
参数：h
Numeric variable for the height of the eic and boxplots that are printed out.
EIC和打印出来的盒状图的高度为数字变量。
参数：w
Numeric variable for the width of the eic and boxplots print out made.
EIC和盒状图的宽度的数字变量打印出来。
参数：...
optional arguments to be passed to mt.teststat
可选参数被传递mt.teststat的
Details
详情----------Details----------
This method handles creation of summary reports with statistics about which analytes were most significantly different between two sets of samples. It computes Welch's two-sample t-statistic for each analyte and ranks them by p-value. It returns a summary report that can optionally be written out to a tab-separated file.
此方法处理创造总结报告与统计分析物，哪些是最显着两组样品之间的不同。计算每个待测韦尔奇的两样本t-统计量和p值排名。它返回一个总结报告，可以随意写出一个制表符分隔的文件。
Additionally, it does all the heavy lifting involved in creating superimposed extracted ion chromatograms for a given number of analytes. It does so by reading the raw data files associated with the samples of interest one at a time. As it does so, it prints the name of the sample it is currently reading. Depending on the number and size of the samples, this process can take a long time.
此外，它创造一个分析物的数量叠加的提取离子色谱所涉及的所有繁重。它这样做是通过阅读相关感兴趣的一个样本的原始数据文件的时间。当它这样做，它打印的样品，目前正在读的名字。根据样品的数量和规模上，这个过程可能需要很长一段时间。
If a base file name is provided, the report (see Value section) will be saved to a tab separated file. If EICs are generated, they will be saved as 640x480 PNG files in a newly created subdirectory. However this parameter can be changed with the commands arguments. The numbered file names correspond to the rows in the report.
如果基本文件名，提供的报告（见价值部分）将被保存到一个制表符分隔的文件。如果EICs产生，他们将被保存为640x480的PNG文件在一个新创建的子目录。然而，这个参数可以改变的命令参数。编号的文件名对应报告中的行。
Chromatographic traces in the EICs are colored and labeled by their sample class. Sample classes take their color from the current palette. The color a sample class is assigned is dependent its order in the xcmsSet object, not the order given in the class arguments. Thus levels(sampclass(object))[1] would use color palette()[1] and so on. In that way, sample classes maintain the same color across any number of different generated reports.
在EICs色谱痕迹的颜色和标记他们的样品类。示例类从当前调色板的颜色。分配样本类的颜色是依赖其命令xcmsSet对象，而不是在类参数给定的顺序。因此levels(sampclass(object))[1]会用颜色palette()[1]等。这样一来，样本类保持相同颜色的跨任意数量的不同生成报告。
When there are multiple sample classes, xcms will produce boxplots of the different classes and will generate a single anova p-value statistic. Like the eic's the plot number corresponds to the row number in the report.
当有多个样品类，xcms会产生不同类别的盒状图，并会生成一个单一的ANOVA p值统计。如EIC的积数对应到报告中的行数。
值----------Value----------
A data frame with the following columns:
与下面的列的数据框：
参数：fold
mean fold change (always greater than 1, see tstat for which set of sample classes was higher)
平均倍数变化（总是大于1，看到tstat这一套样品类较高）
参数：tstat
Welch's two sample t-statistic, positive for analytes having greater intensity in class2, negative for analytes having greater intensity in class1
韦尔奇的两个样本t-统计，积极为有更大的力度，在class2的分析物，分析物具有更大的强度class1负
参数：pvalue
p-value of t-statistic
P-t-统计值
参数：anova
p-value of the anova statistic if there are multiple classes
P-值的ANOVA统计，如果有多个类
参数：mzmed
median m/z of peaks in the group
中位数M / z在该组峰
参数：mzmin
minimum m/z of peaks in the group
最小m / z在该组峰
参数：mzmax
maximum m/z of peaks in the group
组峰最大的m / z
参数：rtmed
median retention time of peaks in the group
在该组峰的保留时间中位数
参数：rtmin
minimum retention time of peaks in the group
在该组最低峰的保留时间
参数：rtmax
maximum retention time of peaks in the group
在该组最大峰的保留时间
参数：npeaks
number of peaks assigned to the group
分配给该组的峰
参数：Sample Classes
number samples from each sample class represented in the group
从每个样品类样本代表在组
参数：metlin
A URL to metlin for that mass
METLIN，大规模的URL
参数：...
one column for every sample class
一列，每一个样本类
参数：Sample Names
integrated intensity value for every sample
每个样品的综合强度值
参数：...
one column for every sample
一列每个样品
方法----------Methods----------
diffreport(object, class1 = levels(sampclass(object))[1], class2 = levels(sampclass(object))[2], filebase = character(), eicmax = 0, eicwidth = 200, sortpval = TRUE, classeic = c(class1,class2), value=c("into","maxo","intb"), metlin = FALSE, h=480,w=640, ...)
diffreport(object, class1 = levels(sampclass(object))[1], class2 = levels(sampclass(object))[2], filebase = character(), eicmax = 0, eicwidth = 200, sortpval = TRUE, classeic = c(class1,class2), value=c("into","maxo","intb"), metlin = FALSE, h=480,w=640, ...)
参见----------See Also----------
xcmsSet-class, mt.teststat, palette
xcmsSet-class，mt.teststat，palette
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 16:04:07
